public InteractionCluster(String miqlQuery, String querySource, int queryStart, int queryRange, String mappingIdDbNames){ super(queryStart, queryRange, mappingIdDbNames); this.addMIQLQuery(miqlQuery); this.addQuerySource(querySource); }
public void addMIQLQuery(String miqlQuery){ addQueryAcc(miqlQuery); }
public List<String> getMIQLQueries() { return getQueryAccs(); }
@Override public void saveResultsInMitab(String fileName) throws IOException { PsimiTabWriter writer = new PsimiTabWriter(); File file = new File(fileName); BufferedWriter bufferedWriter = new BufferedWriter(new FileWriter(file)); try{ Map<Integer, EncoreInteraction> interactionMapping = getInteractionMapping(); Encore2Binary iConverter = new Encore2Binary(getMappingIdDbNames()); for(Integer mappingId:interactionMapping.keySet()){ EncoreInteraction eI = interactionMapping.get(mappingId); BinaryInteraction bI = iConverter.getBinaryInteractionForScoring(eI); writer.write(bI, bufferedWriter); } } finally { bufferedWriter.close(); } }
public void setQuerySourcesFromPsicquicRegistry() { PsicquicRegistryClient registryClient = new DefaultPsicquicRegistryClient(); try { List<ServiceType> allServices = registryClient.listServices(); for (final ServiceType service : allServices) { if (service.isActive()) { this.addQuerySource(service.getName()); } } } catch (PsicquicRegistryClientException e) { logger.error(e); e.printStackTrace(); } }
public void setMIQLQueries(List<String> miqlQueries) { setQueryAccs(miqlQueries); }
protected void runService(MIScore scoreGenerator) { logger.debug("runService"); if(scoreGenerator.isUseOls() == false){ MIO = new MIOntology(false); } super.runService(); processScore(); }
mappingEcoreInteraction.addExperimentToPubmed(encoreInteraction.getExperimentToPubmed()); mappingEcoreInteraction.addExperimentToDatabase(encoreInteraction.getExperimentToDatabase()); processMethodAndType(encoreInteraction, mappingEcoreInteraction); mappingEcoreInteraction.addAuthors(encoreInteraction.getAuthors()); mappingEcoreInteraction.addConfidenceValues(encoreInteraction.getConfidenceValues());
public void setImexSources() { PsicquicRegistryClient registryClient = new DefaultPsicquicRegistryClient(); try { List<ServiceType> allServices = registryClient.listServices(); for (final ServiceType service : allServices) { List<String> tags = service.getTags(); if (service.isActive() && tags != null) { if(tags.contains("MI:0959")){ this.addQuerySource(service.getName()); } } } } catch (PsicquicRegistryClientException e) { logger.error(e); e.printStackTrace(); } }
public InteractionCluster(String miqlQuery, String querySource, String mappingIdDbNames){ super(mappingIdDbNames); this.addMIQLQuery(miqlQuery); this.addQuerySource(querySource); }
public InteractionCluster(String miqlQuery, String querySource){ super(0, 200); this.addMIQLQuery(miqlQuery); this.addQuerySource(querySource); }
public InteractionCluster(String miqlQuery, String querySource, int queryStart, int queryRange){ super(queryStart, queryRange); this.addMIQLQuery(miqlQuery); this.addQuerySource(querySource); }